A mini-Tn5 insertion into a ciprofloxacin (CIP)-resistant mutant of Vibrio cholerae O1 revealed that overexpression of the vca0421 gene, which encodes a hypothetical protein, in the CIP-resistant mutant carrying a mutation in the quinolone resistance-determining region (QRDR) of the gyrA gene causes sensitization to CIP. We propose a new intrinsic mechanism of resistance to fluoroquinolones due to the inherently reduced expression of the vca0421 gene in V. cholerae O1.